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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_004538
Reference: OH-1004 Chr: Chr01 Coordinates: 139675338-139677182 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1845 bp · LXL04_004538|LXL04_004538|OH1004|cDNA

ATGGAGCGTAAAATGCTCAGGTTCTTGCAATCATGCAAAAACGTCAATCACTTGAAGCAAACCCATCTCCAGATACTCGTCAATGGCCTCAATGACAATAACTATCTACTTCAAAATCTCATCGCGTTTTCGTCTGACGTCATTTCACTTGATTATGCTTTCAGTGTGCTTCAAACTTCGAATTCTCCCGACGTTGTTGTTTATAATACAATGATCAAATCCTTCATCACCAATAAAAGCAATTGTACCCCATATAAAGC...

CDS

Download CDS FASTA

1845 bp · LXL04_004538|LXL04_004538|OH1004|CDS

ATGGAGCGTAAAATGCTCAGGTTCTTGCAATCATGCAAAAACGTCAATCACTTGAAGCAAACCCATCTCCAGATACTCGTCAATGGCCTCAATGACAATAACTATCTACTTCAAAATCTCATCGCGTTTTCGTCTGACGTCATTTCACTTGATTATGCTTTCAGTGTGCTTCAAACTTCGAATTCTCCCGACGTTGTTGTTTATAATACAATGATCAAATCCTTCATCACCAATAAAAGCAATTGTACCCCATATAAAGC...

Protein

Download Protein FASTA

614 aa · LXL04_004538|LXL04_004538|OH1004|PROTEIN

MERKMLRFLQSCKNVNHLKQTHLQILVNGLNDNNYLLQNLIAFSSDVISLDYAFSVLQTSNSPDVVVYNTMIKSFITNKSNCTPYKALSVYKELRSRAFSVSPNSFTFTFLLKCFEVLDVGRMIHGEVLKMGLDSSSVFVQNTLLNFYAKCGNDGVDLARKVFDEMTIRDTVSWNTMIGIHMDCQEVESAIKLFESMPKRSVVTWNSVITGLAKNGNMQSARSLFDKMPEKNEVSWNCLISGYVKSGDLKNAEIMFNNMP...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

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ID Mapping

Input IDLXL04_004538
TK1151 IDTkA01G136720
OH-1004 IDLXL04_004538
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)78.500
Protein coverage (%)TK1151 92.683 / OH-1004 32.085
Coverage and evidence

Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.

Source versionOH-1004 / GCA_047496595.1_OSU_TarKok_2.0
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDLXL04_004538
LocationChr01:139675338-139677182 (-)
DescriptionSimilar to PCMP-E28: Pentatricopeptide repeat-containing protein At2g22410, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At2g22410 Pentatricopeptide repeat-containing protein At2g22410, mitochondrial. No verified direct reference in this release
At3g29230 Pentatricopeptide repeat-containing protein At3g29230. No verified direct reference in this release
At3g15930 Putative pentatricopeptide repeat-containing protein At3g15930. No verified direct reference in this release
At2g29760 Involved in RNA editing event in chloroplasts.
A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472
At2g45350 Plays a major role in chloroplast RNA editing.
A pentatricopeptide repeat protein is a site recognition factor in chloroplast RNA editing.2006 · DOI: 10.1074/jbc.m608184200
Two interacting proteins are necessary for the editing of the NdhD-1 site in Arabidopsis plastids.2012 · DOI: 10.1105/tpc.112.099507

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_004538 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0016556 mRNA modification Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:1900865 chloroplast RNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0005773 vacuole Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT2G22410
ath:AT2G29760
ath:AT2G45350
ath:AT3G15930
ath:AT3G29230
These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.
Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene
Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Mitochondrion0.652
Rank 1 · LXL04_004538 · OH-1004
Plastid0.159
Rank 2 · LXL04_004538 · OH-1004
Nucleus0.056
Rank 3 · LXL04_004538 · OH-1004
Cytoplasm0.038
Rank 4 · LXL04_004538 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_004538 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF13041.13PPR_263-115 aa
PF13041.13PPR_2169-202 aa
PF13041.13PPR_2201-232 aa
PF12854.14PPR_1201-228 aa
PF01535.27PPR203-232 aa
PF13041.13PPR_2232-259 aa
PF12854.14PPR_1232-259 aa
PF01535.27PPR234-259 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_004538PF13041.13PPR_2631153.3e-72239.1
LXL04_004538PF13041.13PPR_21692023.3e-72239.1
LXL04_004538PF13041.13PPR_22012323.3e-72239.1
LXL04_004538PF12854.14PPR_12012285e-47158.0
LXL04_004538PF01535.27PPR2032324e-63206.1
LXL04_004538PF13041.13PPR_22322593.3e-72239.1
LXL04_004538PF12854.14PPR_12322595e-47158.0
LXL04_004538PF01535.27PPR2342594e-63206.1
LXL04_004538PF13812.13PPR_32653111.7e-2692.8
LXL04_004538PF12854.14PPR_12953245e-47158.0
LXL04_004538PF13041.13PPR_22963453.3e-72239.1
LXL04_004538PF01535.27PPR2993254e-63206.1
LXL04_004538PF13041.13PPR_23994453.3e-72239.1
LXL04_004538PF01535.27PPR4014304e-63206.1
LXL04_004538PF20431.5E_motif5165786.6e-1349.4

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9SJZ3Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g22410, mitochondrial37.903%Swiss-Protmoderate database homology
Q9LS72Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g2923034.711%Swiss-Protmoderate database homology
Q9LSB8Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At3g1593035.818%Swiss-Protmoderate database homology
O82380Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g29760, chloroplastic34.309%Swiss-Protmoderate database homology
O22137Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g45350, chloroplastic36.789%Swiss-Protmoderate database homology

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